1JSD | pdb_00001jsd

CRYSTAL STRUCTURE OF SWINE H9 HAEMAGGLUTININ

• PDB DOI: https://doi.org/10.2210/pdb1JSD/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/swine/Hong Kong/9/98(H9N2))
• Mutation(s): No 


• Deposited: 2001-08-17 Released: 2001-09-26 
• Deposition Author(s): Ha, Y., Steven, D.J., Skehel, J.J., Wiley, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.230 (Depositor) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

H5 avian and H9 swine influenza virus haemagglutinin structures: possible origin of influenza subtypes.

Ha, Y., Stevens, D.J., Skehel, J.J., Wiley, D.C.

(2002) EMBO J 21: 865-875

• PubMed: 11867515 
• DOI: https://doi.org/10.1093/emboj/21.5.865
• Primary Citation Related Structures: 
  1JSD, 1JSM


• PubMed Abstract: 
  

  There are 15 subtypes of influenza A virus (H1-H15), all of which are found in avian species. Three caused pandemics in the last century: H1 in 1918 (and 1977), H2 in 1957 and H3 in 1968. In 1997, an H5 avian virus and in 1999 an H9 virus caused outbreaks of respiratory disease in Hong Kong. We have determined the three-dimensional structures of the haemagglutinins (HAs) from H5 avian and H9 swine viruses closely related to the viruses isolated from humans in Hong Kong. We have compared them with known structures of the H3 HA from the virus that caused the 1968 H3 pandemic and of the HA--esterase--fusion (HEF) glycoprotein from an influenza C virus. Structure and sequence comparisons suggest that HA subtypes may have originated by diversification of properties that affected the metastability of HAs required for their membrane fusion activities in viral infection.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.51 kDa 
• Atom Count: 4,136 
• Modeled Residue Count: 477 
• Deposited Residue Count: 495 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HAEMAGGLUTININ (HA1 CHAIN)	A	319	Influenza A virus (A/swine/Hong Kong/9/98(H9N2))	Mutation(s): 0
UniProt
Find proteins for Q91CD4 (Influenza A virus) Explore Q91CD4  Go to UniProtKB:  Q91CD4
Glycosylation
Glycosylation Sites: 4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HAEMAGGLUTININ (HA2 CHAIN)	B	176	Influenza A virus (A/swine/Hong Kong/9/98(H9N2))	Mutation(s): 0
UniProt
Find proteins for Q91CD4 (Influenza A virus) Explore Q91CD4  Go to UniProtKB:  Q91CD4
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.230 (Depositor) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.5	α = 90
b = 108.5	β = 90
c = 149.3	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-09-26 
Deposition Author(s): Ha, Y., Steven, D.J., Skehel, J.J., Wiley, D.C.

Revision History  

• Version 1.0: 2001-09-26
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary